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Species loss in fragile insular communities can alter the composition and stability of local assemblages. Climate change or anthropogenic pressures are sometimes attributed to the loss of Caribbean bats, but other factors are elusive to document. We studied time-scaled changes in bat assemblage composition from a palaeontological excavation in Cueva Matos, Puerto Rico. Over 800 individual fossils were identified to species, and charcoal was used to develop an AMS¹⁴C chronology. Although three bat species live in the cave today, fossils comprise 10 species. These included five extirpated species from the cave and three no longer present on the island. Losses centred around 2460–4470 kya. Notably, we document the first record ofMormoops megalophyllaas extirpated from Puerto Rico. Nearly 90% of the extirpated bats in Cueva Matos prefer to roost in hot caves where temperatures may reach 40℃. However, these temperatures are currently not held in any cave chamber. Our findings suggest that structural changes in the cave resulted in the loss of heat traps and likely led to a sudden shift in the bat assemblage composition at this cave, which is now void of hot cave specialist bats.